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DAT BIO > DAT bio chapter 6 > Flashcards

DAT bio chapter 6 Flashcards

1
Q

Nucleotide

A

ribose sugar, nitrogenous base, and

phosphate group.

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2
Q

Nucleoside

A
  • ribose sugar and nitrogenous base.
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3
Q

DNA is a polymer of what

A

nucleotides

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4
Q

DNA has what on the 2 carbon on the ribose sugar

A

hydrogen

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5
Q

RNA has what on the 2 carbon on the ribose sugar

A

OH (hydroxyl group

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6
Q

In DNA. Adenine binds to what with how many bonds

A

Thymine

2 hydrogen bonds

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7
Q

In DNA. Guanine binds to what with how many bonds

A

cytosine

3 hydrogen bonds

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8
Q

In RNA, adenine binds to what

A

uracil

2 hydrogen bodns

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9
Q

T/F greater temp is needed to break the G-C bonds

A

true, due to more bonds

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10
Q

What are nucleosomes

A

are complexes of DNA wrapped

around histone proteins.

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11
Q

How many histones do each nucleosomes contain?

A

9

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12
Q

The central core of the nucleosome contains how many of each histone?

A

contains two

of each histone H2A, H2B, H3 and H4.

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13
Q

T/F On the
outside of the nucleosome, a single histone, H1, holds the DNA in
place.

A

true

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14
Q

Chromatin

A

Functions in condensing the the structure of dna and his tones into a more compact structure

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15
Q

Two types of chromatin

A
  1. Euchromatin

2. Heterochromatin

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16
Q

Euchromatin

A

nucleosomes are “loosely
packed”, so DNA is readily accessible for
transcription.

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17
Q

Heterochromatin

A

nucleosomes are “tightly

packed”, so DNA is mostly inactive.

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18
Q

what charges are histones and DNA

A

Histones are positively charged while DNA is

negatively charged, allowing proper binding.

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19
Q

Acetylation of histones does what

A

removes positive charges,
relaxing DNA-histone attractions and allowing for
more transcription to happen.

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20
Q

Deacetylation of histones does what

A

increases positive
charges, tightening DNA-histone attractions and
decreasing transcription.

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21
Q

Methylation of histones does what

A

adds methyl groups,

either increasing or decreasing transcription.

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22
Q

What is the origin of replication?

A

required to initiate DNA

replication where the DNA strands first separate.

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23
Q

Multiple vs single origin of replication

A

Organisms with circular DNA such as bacteria
have a single origin of replication while organisms
with linear DNA such as humans have multiple
origins of replication.

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24
Q

What does it mean for DNA to undergo semiconservative replication?

A

it means the each new double helix produced by
replication has one “new” strand and one “old”
strand.

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25
Q

What does it mean for DNA to be antiparallel

A

5’ end
(terminal phosphate group) of one strand is
always next to the 3’ end (terminal hydroxyl
group) of the other strand and vice versa.

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26
Q

Steps of DNA replication

A
  1. initiation
  2. elongation
  3. termination
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27
Q

Step 1 of DNA replication

- initiation

A
  • creating origins of replication at
    A-T rich segments of DNA because A-T bonds
    only have two hydrogen bonds and are easier
    to split apart.
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28
Q

Step 2 of DNA replication

- Elongation

A

producing new DNA strands using

different types of enzymes.

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29
Q 
Elongation 1
(helicase)
A

Helicase unzips DNA by breaking hydrogen
bonds between strands, creating a
replication fork.

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30
Q 
Elongation 2
(Single-strand binding proteins)
A

bind to
uncoiled DNA strands, preventing
reattachment of the strands to each other.

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31
Q

Elongation 3

Topoisomerase

A

nicks the DNA double
helix ahead of helicase to relieve built-up
tension.

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32
Q

Elongation 4

Primase

A

places RNA primers at the origin
of replication to create 3’ ends for
nucleotide addition.

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33
Q

Elongation 5

Sliding clamp proteins

A

hold DNA

polymerase onto the template strand.

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34
Q

Elongation 6

DNA polymerase

A

Enzyme that extends dna in the 5 to 3 direction

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35
Q

Elongation 7

The leading strand

A

produced
continuously because it has a 3’ end that
faces the replication fork.

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36
Q

Elongation 8

● The lagging strand

A

is produced
discontinuously because its 3’ end is facing
away from the replication fork. Thus, many
RNA primers are needed to produce short
DNA fragments called Okazaki fragments.

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37
Q

Elongation 9

A different DNA polymerase

A

replaces RNA

primers with DNA.

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38
Q

Elongation 10

DNA ligase

A

glues separated fragments of

DNA together.

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39
Q

Termination

A

replication fork cannot

continue, ending DNA replication.

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40
Q

Termination part 1

Telomeres

A

are noncoding, repeated
nucleotide sequences at the ends of linear
chromosomes. They are necessary in
eukaryotes because when the replication
fork reaches the end of a chromosome, a
small segment of DNA from the telomere is
not replicated and lost (no RNA primer is
present to help produce another Okazaki
fragment).

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41
Q

Termination part 2

Telomerase

A

enzyme that extends

telomeres to prevent DNA loss.

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42
Q

DNA replication happens in which part of the cell cycle

A

S phase

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43
Q

Summary of transcription

A

Genes are instructions within DNA that code for
proteins. However, they must first be transcribed
into RNA before being translated into proteins.

Specifically, DNA undergoes transcription to
produce single-stranded messenger RNA (mRNA).

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44
Q

Steps for transcription

A

Initiation
Elongation
Termination -

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45
Q

Initiation for transcription

A

a promoter sequence (aka
promoter) next to the gene attracts RNA
polymerase to transcribe the gene.

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46
Q

Initiation for elongation

A
  • transcription bubble forms and
    RNA polymerase travels in the 3’ → 5’ direction
    on the template strand. However, it extends
    RNA in the 5’ → 3’ direction.
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47
Q

Initiation for Termination -

A

a termination sequence (aka
terminator) signals to RNA polymerase to
stop transcribing the gene.

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48
Q

Where does transcription happen in the prokaryotes

A

cytosol

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49
Q

First step of transcription in prokaryotes

A

RNA polymerase opens up DNA, forming a

transcription bubble.

50
Q

second step of transcription in prokaryotes

A

Before transcription can occur, a sigma factor
combines with prokaryotic core RNA
polymerase to form RNA polymerase
holoenzyme, giving it the ability to target specific
DNA promoter regions.

51
Q

What is an operon?

A

group of genes that function as a

single unit that is controlled by one promoter.

52
Q

what is the operator region?

A

present near the operon’s
promoter and binds activator/repressor
proteins to regulate the promoter.

53
Q

what is lac operon

A 
inducible operon (it must be
induced to become active).
54
Q

What three genes are contained within the lac operon and what do they do

A

LacZ, lacY, and lacA
encode proteins required for lactose
metabolism.

55
Q

When is lac operon used>

A

when glucose is not available as an energy source,

so lactose must be used.

56
Q

First way lac operon can be controlled

A

BY Lac repressor protein

57
Q

What gene encodes for lac repressor protein

A

LACL, which is always on

58
Q

How does lac repressor protein block transcription?

A

by constantly binding to the operator

59
Q

What happens to lac repressor protein when lactose is present?

A

converted to allolactose.

60
Q

What does allolactose do?

A

binds directly to the repressor and
removes it from the operator, allowing
transcription to occur.

61
Q

Second level of lac operon regulation

A

cAMP levels and catabolite activator protein

CAP

62
Q

cAMP levels are ______ related to glucose levels,

A

Inversely,

when glucose is low, cAMP is high.

63
Q

What does cAMP bind to?

A

to catabolite activator protein (CAP), which then
attaches near the lac operon promoter to help
attract RNA polymerase, promoting transcription.

64
Q

Another operon employed by prokaryotes

A

trp operon,

65
Q

trp operon responsible for what

A

producing the

amino acid tryptophan.

66
Q

Try operon is known as….

A

repressible operon because it codes for
tryptophan synthetase and is always active
unless the presence of tryptophan in the
environment represses the operon.

67
Q

Tryptophan binds to

A

trp repressor protein, which then attaches to the operator on the trp
operon to prevent tryptophan production.

68
Q

What happens when tryptophan is not present in the environment>

A

trp operon will undergo transcription because the

trp repressor protein will be inactive.

69
Q

eukaryotic transcription

occurs where

A

occurs in the nucleus and uses RNA polymerase

II to transcribe most genes.

70
Q

what is needed in eukaryotes to help RNA polymerase bind to promoters?

A

Transcription factors

71
Q

what is the tata box>

A

sequence in many promoters that

transcription factors can recognize and bind to.

72
Q

Enhancers

A

DNA sites that activator
proteins can bind to; they help increase
transcription of a gene.

73
Q

Silencers

A

DNA sites that repressor
proteins can bind to; they decrease
transcription of a gene.

74
Q

Where are enhancers and silencers located?

A

far upstream or downstream form the gene. They loop around to colocalize
with RNA polymerase.

75
Q

The poly A signal is located where

A

within the terminator
sequence and stimulates polyadenylation
(addition of adenine nucleotides to the 3’ end of
the mRNA).`

76
Q

Post-transcriptional modification

A

conversion of pre-mRNA into processed mRNA,

which leaves the nucleus.

77
Q

three

main types of post-transcriptional modification:

A

5’ capping
Polyadenylation of the 3’ end
Splicing out introns

78
Q

5’ capping

A
  • 7-methylguanosine cap is added
    to the 5’ end of the mRNA during elongation,
    protecting the mRNA from degradation.
79
Q

Polyadenylation of the 3’ end

A
  • addition of
    the poly A tail to the 3’ end to prevent
    degradation.
80
Q

Splicing out introns

A
  • introns are stretches of
    noncoding DNA that lie between regions of
    coding DNA (exons). Splicing refers to
    removing introns from pre-mRNA using
    spliceosomes. “Splice signals” present within
    introns signal to the spliceosome where to cut.
81
Q

(Eukaryotic Post-Transcriptional Modifications)

snRNAs (small nuclear RNA) and proteins make what

A

the functional part of a spliceosome and are
collectively referred to snRNPs (small nuclear
RiboNucleic Proteins).

82
Q

(Eukaryotic Post-Transcriptional Modifications)

Alternative splicing

A

a single pre-mRNA
having multiple possible spliced mRNA products.
Thus, the same pre-mRNA can produce many
different proteins.

83
Q

Important players in translation

A

Ribosomes and tRNA (transfer RNA) are

84
Q

what is translation

A

process of

converting mRNA into protein products.

85
Q

Ribosomes

A

made up of one small subunit and

one large subunit as described below:

86
Q

eukaryotes ribosomes

A 
small (40S) and large (60S)
subunits form a 80S ribosome. They are
composed of rRNA (ribosomal RNA) and
proteins. The subunits are made in the
nucleolus and assembled once they are
exported to the cytosol.
87
Q

prokaryotes ribosomes

A

small (30S) and large (50S)
subunits form a 70S ribosome. They are also
composed of rRNA and proteins, but are
assembled together in the nucleoid.

88
Q

what is a codon

A

a group of three mRNA bases (A, U, G,
or C) that code for an amino acid or terminate
translation.

89
Q

how many combinations of codon is there

A

64 codon combinations
total but only 20 amino acids, so degeneracy is
present (multiple codons code for the same amino
acid).

90
Q

Start codon:

A

AUG

91
Q

STOP CODON

A

UAA, UAG, UGA

92
Q

what is an anticodon

A

group of three tRNA bases (A,
U, G, or C) that base pairs with a codon. Each tRNA
carries an amino acid to be added to the growing
protein.

93
Q

Aminoacyl-tRNA

A

tRNA bound to an

amino acid.

94
Q

Aminoacyl-tRNA synthetase

A

enzyme that
attaches an amino acid to a specific tRNA using the
energy from ATP.

95
Q

Ribosomal binding sites for tRNA:

A

A site - A for aminoacyl-tRNA, which first
enters at this site.
2. P site - P for peptidyl-tRNA, which carries the
growing polypeptide.
3. E site - E for exit site. The tRNA from the P site
is sent here and released from the ribosome.

96
Q

The ribosome catalyzes the formation of what

A

a peptide
bond between the polypeptide in the P site and
the newly added amino acid in the A site.

97
Q

What happens after the formation of a peptide bond between the polypeptide in the p site and the newly added amino acid in the a site

A

the polypeptide is transferred to the A
site’s tRNA and the ribosome shifts one codon
down the mRNA. The A site will now be empty and
ready to accept another aminoacyl-tRNA. The tRNA
from the P site will be transferred to the E site and
will leave the ribosome.

98
Q

What is DNA mutation

A

a heritable change in the
DNA nucleotide sequence that can be passed
down to daughter cells.

99
Q

Three main types of DNA mutations:

A

Base substitutions (point mutations)
Insertions
Deletions -

100
Q

Base substitutions (point mutations)

A

one nucleotide is replaced by another.

101
Q

Silent mutations

part of base substitutions

A 
no change in
amino acid sequence. Due to “third
base wobble”, mutations in the DNA
sequence that affect the third base of
a codon can still result in the same
amino acid being added to the
protein. Relies on the degeneracy
(redundancy) of translation.
102
Q

Missense mutations

part of base substitutions

A 
single change in
amino acid sequence. Can either be
conservative (mutated amino acid similar
to unmutated) or non-conservative
(mutated amino acid different from
unmutated).
103
Q

Nonsense mutation

part of base substitutions

A
  • single change in
    amino acid sequence that results in a stop
    codon. Results in early termination of
    protein.
104
Q

Insertions

A
  • adding nucleotides into the DNA

sequence - can shift the reading frame.

105
Q

Deletions

A

removing nucleotides from the

DNA sequence - can shift the reading frame.

106
Q

Factors that contribute to DNA mutations:

A 
DNA polymerase errors during DNA
replication.
 Loss of DNA during meiosis crossing over.
 Chemical damage from drugs.
Radiation.
107
Q

Factors that prevent DNA mutations:

A 
● DNA polymerase proofreading by DNA
polymerase.
● Mismatch repair machinery that checks
uncaught errors.
● Nucleotide excision repair that cuts out
damaged DNA and replaces it with correct
DNA using complementary base pairing.
108
Q

Are viruses living or non living

A

non living, they must infect living cells to multiply

109
Q

capsid (virus)

A

viral protein coat that is made of

subunits called capsomeres.

110
Q

phospholipid envelope

A

some viruses pick this up

from the host cell membrane.

111
Q

Two viral life cycle types:

A

lysogenic

lytic

112
Q

Lysogenic cycle

A

virus is considered dormant
because it inserts its own genome into the
host’s genome and does not harm the host.
Each time the host genome undergoes
replication, so does the viral genome.

113
Q

Lytic cycle

A

virus takes over host to replicate
and does cause harm to the host. The viral
particles produced can lyse the host cell to
find other hosts to infect.

114
Q

Bacteria are what and how do they divide

A

asexual
binary fission
so they only receive genes from one parent cell
and do not increase genetic diversity through
reproduction.

115
Q

How do bacteria must increase genetic diversity

A

through horizontal gene transfer

116
Q

What is horizontal gene transfer

A

the transfer of genes between individual

organisms.

117
Q

three methods of

horizontal gene transfer:

A

Conjugation
transformation
transduction

118
Q

Conjugation

A

bacteria use a cytoplasmic
bridge called a pili to copy and transfer a
special plasmid known as the F plasmid
(fertility factor). If a bacteria contains an F
plasmid, it is referred to as F+. If not, it is
referred to as F-. To review, plasmids are
circular DNA pieces that are independent from
a bacteria’s single circular chromosome.

119
Q

transformation

A

bacteria take up extracellular
DNA. Bacteria are referred to as competent if
they can perform transformation.
Electroporation is the process of using
electrical impulses to force bacteria to become
competent.

120
Q

Transduction

A

viruses transfer bacterial DNA
between different bacterial hosts. This occurs
when a bacteriophage enters the lysogenic
cycle in its host and carries bacterial DNA
along with its own genome upon re-entering
the lytic cycle.

DAT BIO (25 decks)

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